Error Message Running Cufflinks On Local Galaxy

Question: Error Message Running Cufflinks On Local Galaxy

5.8 years ago by

Dear Jen, I have downloaded Galaxy on my computer. When trying to run cufflinks locally I have this error message: 8: Cufflinks on data 3 and data 2: gene expression error An error occurred running this job:Could not determine Cufflinks version cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.150000 -p 4 -G /Users/davidedegliesposti/galaxy- dist/database/files/000/dataset_2.dat -N Error running cufflinks. return code = 127 /bin/sh: cufflinks: command May this be due to an error of installation? Thank you for your help Davide Davide Degli Esposti, PhD Epigenetic (EGE) Group International Agency for Research on Cancer Tel. +33 4 72738036 Fax. +33 4 72738322 150, cours Albert Thomas 69372 Lyon Cedex 08 France This message and its attachments are strictly confidential. If you are not the intended recipient of this message, please immediately notify the sender and delete it. Since its integrity cannot be guaranteed, its content cannot involve the sender's responsibility. Any misuse, any disclosure or publication of its content, either whole or partial, is prohibited, exception made of formally approved use

rna-seq cufflinks • 1.1k views

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modified 2.9 years ago by hoonilk • 0 • written 5.8 years ago by Davide Degli Esposti • 80

5.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Davide, Is this a job that can be executed on the public Galaxy Main instance (same inputs/settings)? If so, and the error is reproducible, let's review it as a bug report and determine if the there is a data or other issue. Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

ADD COMMENT • link modified 2.9 years ago • written 5.8 years ago by Jennifer Hillman Jackson ♦ 25k

2.9 years ago by

hoonilk • 0

hoonilk • 0 wrote:

Did you solve the problem?

I have exactly same problem.

ADD COMMENT • link written 2.9 years ago by hoonilk • 0

Hello,

Was the problem also on a local? Is the version of Galaxy current? Did the tool installation use managed dependencies? In the admin tool list, are any problems noted (perhaps missing dependencies)? Is this one of the first tools installed/used in your instance or have other installed tools run successfully in the past?

I do not recall the exact solution to this prior problem. I suspect it was a tool installation problem (the initial report above was made prior to the implementation of managed dependencies across common tool installs from the Tool Shed).

When you reply, please share the details of your local configuration and tool install process as a new question. You can reference this post in your question. Much has changed in three years and starting over in a new thread would be best.

Thanks, Jen, Galaxy team

ADD REPLY • link written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k

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